Iodine in PDB 4p4v: Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Maa)Avk

The structure of Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Maa)Avk, PDB code: 4p4v was solved by R.K.Spencer, J.S.Nowick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.30 / 1.97
Space group	P 42 2 2
Cell size a, b, c (Å), α, β, γ (°)	62.030, 62.030, 44.676, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 22.2

The structure of Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Maa)Avk also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Iodine atom in the Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Maa)Avk (pdb code 4p4v). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 3 binding sites of Iodine where determined in the Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Maa)Avk, PDB code: 4p4v:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in the Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Maa)Avk


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Maa)Avk within 5.0Å range: probe atom residue distance (Å) B Occ A:I5 b:40.2 occ:1.00 I A:PHI5 0.0 40.2 1.0 CZ A:PHI5 2.1 57.2 1.0 CE1 A:PHI5 3.0 57.1 1.0 CE2 A:PHI5 3.1 61.2 1.0 HE1 A:PHI5 3.1 68.5 1.0 HE2 A:PHI5 3.1 73.5 1.0 HB2 C:LEU3 3.5 55.2 1.0 O C:LEU3 3.5 31.5 1.0 H C:PHI5 3.6 41.6 1.0 HD2 C:PHI5 3.7 61.7 1.0 HA C:LEU4 3.8 46.4 0.6 HA C:LEU4 3.8 46.4 0.4 CD2 C:PHI5 3.9 51.4 1.0 C C:LEU3 3.9 34.1 1.0 HB2 C:PHI5 4.0 65.3 1.0 N C:PHI5 4.0 34.6 1.0 CG C:PHI5 4.2 52.6 1.0 HB3 C:LEU3 4.2 55.2 1.0 N C:LEU4 4.2 34.8 0.6 N C:LEU4 4.2 35.8 0.4 CA C:LEU4 4.3 38.6 0.6 CB C:LEU3 4.3 46.0 1.0 CA C:LEU4 4.3 38.6 0.4 C C:LEU4 4.3 38.0 0.6 C C:LEU4 4.3 38.0 0.4 CD1 A:PHI5 4.3 51.6 1.0 CE2 C:PHI5 4.3 44.1 1.0 CD2 A:PHI5 4.4 58.7 1.0 CB C:PHI5 4.5 54.4 1.0 HE2 C:PHI5 4.5 52.9 1.0 HB2 A:MAA13 4.7 53.7 1.0 H C:LEU4 4.8 41.7 0.6 H C:LEU4 4.8 43.0 0.4 CA C:LEU3 4.8 33.9 1.0 CA C:PHI5 4.9 34.2 1.0 CG A:PHI5 4.9 45.0 1.0 HD12 C:LEU3 4.9 99.1 1.0 CD1 C:PHI5 5.0 56.4 1.0

Iodine binding site 2 out of 3 in the Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Maa)Avk


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Maa)Avk within 5.0Å range: probe atom residue distance (Å) B Occ B:I5 b:38.3 occ:1.00 I B:PHI5 0.0 38.3 1.0 CZ B:PHI5 2.1 45.3 1.0 CE1 B:PHI5 3.1 51.1 1.0 CE2 B:PHI5 3.1 55.0 1.0 HE1 B:PHI5 3.1 61.3 1.0 HE2 B:PHI5 3.1 66.0 1.0 CD1 B:PHI5 4.3 55.7 1.0 CD2 B:PHI5 4.4 57.1 1.0 HB2 B:MAA13 4.7 49.5 1.0 CG B:PHI5 4.9 46.6 1.0

Iodine binding site 3 out of 3 in the Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Maa)Avk


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Maa)Avk within 5.0Å range: probe atom residue distance (Å) B Occ C:I5 b:38.4 occ:1.00 I C:PHI5 0.0 38.4 1.0 CZ C:PHI5 2.1 41.5 1.0 CE1 C:PHI5 3.1 51.7 1.0 CE2 C:PHI5 3.1 44.1 1.0 HE1 C:PHI5 3.1 62.1 1.0 HE2 C:PHI5 3.1 52.9 1.0 HA B:TYR6 3.3 40.0 1.0 HG22 B:THR7 3.3 42.7 1.0 HB3 B:PHI5 3.5 38.4 1.0 O A:LEU3 3.5 35.9 1.0 HB2 A:LEU3 3.5 38.0 1.0 O B:PHI5 3.6 30.9 1.0 HG13 B:VAL11 3.6 45.9 1.0 H A:PHI5 3.8 35.1 1.0 HA A:LEU4 3.8 45.3 0.3 HA A:LEU4 3.8 45.6 0.7 C B:PHI5 3.9 29.9 1.0 C A:LEU3 3.9 32.5 1.0 CA B:TYR6 4.0 33.3 1.0 HD2 A:PHI5 4.0 70.4 1.0 HB2 B:PHI5 4.0 38.4 1.0 CD2 A:PHI5 4.0 58.7 1.0 HB2 A:PHI5 4.1 42.3 1.0 N B:TYR6 4.1 31.6 1.0 N A:PHI5 4.1 29.2 1.0 HG22 B:VAL11 4.1 61.0 1.0 CB B:PHI5 4.1 32.0 1.0 N A:LEU4 4.2 35.5 0.7 H B:THR7 4.2 43.1 1.0 CG2 B:THR7 4.2 35.6 1.0 N A:LEU4 4.2 35.8 0.3 C B:TYR6 4.3 33.6 1.0 CG A:PHI5 4.3 45.0 1.0 HB3 A:LEU3 4.3 38.0 1.0 CB A:LEU3 4.3 31.7 1.0 CA A:LEU4 4.3 37.8 0.3 CA A:LEU4 4.3 38.0 0.7 N B:THR7 4.3 35.9 1.0 HG11 B:VAL11 4.3 45.9 1.0 HG21 B:THR7 4.3 42.7 1.0 C A:LEU4 4.3 34.5 0.3 C A:LEU4 4.3 34.5 0.7 HB B:THR7 4.3 47.3 1.0 CD1 C:PHI5 4.3 56.4 1.0 CD2 C:PHI5 4.4 51.4 1.0 CG1 B:VAL11 4.4 38.3 1.0 CE2 A:PHI5 4.5 61.2 1.0 CB A:PHI5 4.6 35.2 1.0 H B:TYR6 4.6 38.0 1.0 H A:LEU4 4.6 42.7 0.7 HB2 C:MAA13 4.7 44.6 1.0 CA B:PHI5 4.7 27.5 1.0 HG21 B:VAL11 4.7 61.0 1.0 H A:LEU4 4.7 43.0 0.3 CA A:LEU3 4.7 29.2 1.0 HE2 A:PHI5 4.7 73.5 1.0 CB B:THR7 4.8 39.4 1.0 CG2 B:VAL11 4.8 50.8 1.0 CG C:PHI5 4.9 52.6 1.0 HG23 B:THR7 4.9 42.7 1.0 O B:TYR6 4.9 33.0 1.0 HB3 C:MAA13 4.9 44.6 1.0 CD1 A:PHI5 4.9 51.6 1.0 CA A:PHI5 4.9 29.6 1.0

R.K.Spencer, A.G.Kreutzer, P.J.Salveson, H.Li, J.S.Nowick. X-Ray Crystallographic Structures of Oligomers of Peptides Derived From Beta 2-Microglobulin. J.Am.Chem.Soc. 2015.
ISSN: ESSN 1520-5126
PubMed: 25915729
DOI: 10.1021/JACS.5B01673